MicroRNA Profiling of Fresh Lung Adenocarcinoma and Adjacent Normal Tissues from Ten Korean Patients Using miRNA-Seq
MicroRNA transcriptomes from fresh tumors and the adjacent normal tissues were profiled in 10 Korean patients diagnosed with lung adenocarcinoma using a next-generation sequencing (NGS) technique called miRNA-seq. The sequencing quality was assessed using FastQC, and low-quality or adapter-contamina...
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MDPI AG
2023-05-01
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| Online Access: | https://www.mdpi.com/2306-5729/8/6/94 |
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| author | Jihye Park Sae Jung Na Jung Sook Yoon Seoree Kim Sang Hoon Chun Jae Jun Kim Young-Du Kim Young-Ho Ahn Keunsoo Kang Yoon Ho Ko |
| author_facet | Jihye Park Sae Jung Na Jung Sook Yoon Seoree Kim Sang Hoon Chun Jae Jun Kim Young-Du Kim Young-Ho Ahn Keunsoo Kang Yoon Ho Ko |
| author_sort | Jihye Park |
| collection | DOAJ |
| description | MicroRNA transcriptomes from fresh tumors and the adjacent normal tissues were profiled in 10 Korean patients diagnosed with lung adenocarcinoma using a next-generation sequencing (NGS) technique called miRNA-seq. The sequencing quality was assessed using FastQC, and low-quality or adapter-contaminated portions of the reads were removed using Trim Galore. Quality-assured reads were analyzed using miRDeep2 and Bowtie. The abundance of known miRNAs was estimated using the reads per million (RPM) normalization method. Subsequently, using DESeq2 and Wx, we identified differentially expressed miRNAs and potential miRNA biomarkers for lung adenocarcinoma tissues compared to adjacent normal tissues, respectively. We defined reliable miRNA biomarkers for lung adenocarcinoma as those detected by both methods. The miRNA-seq data are available in the Gene Expression Omnibus (GEO) database under accession number GSE196633, and all processed data can be accessed via the Mendeley data website. |
| first_indexed | 2024-03-11T02:35:41Z |
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| issn | 2306-5729 |
| language | English |
| last_indexed | 2024-03-11T02:35:41Z |
| publishDate | 2023-05-01 |
| publisher | MDPI AG |
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| spelling | doaj.art-499141ef86a8470b92846cf286be0f572023-11-18T09:58:23ZengMDPI AGData2306-57292023-05-01869410.3390/data8060094MicroRNA Profiling of Fresh Lung Adenocarcinoma and Adjacent Normal Tissues from Ten Korean Patients Using miRNA-SeqJihye Park0Sae Jung Na1Jung Sook Yoon2Seoree Kim3Sang Hoon Chun4Jae Jun Kim5Young-Du Kim6Young-Ho Ahn7Keunsoo Kang8Yoon Ho Ko9Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Republic of KoreaDepartment of Radiology, Uijeongbu St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of KoreaUijeongbu St. Mary’s Hospital Clinical Research Laboratory, The Catholic University of Korea, Uijeongbu 11765, Republic of KoreaDivision of Medical Oncology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of KoreaDivision of Medical Oncology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of KoreaDepartment of Thoracic and Cardiovascular Surgery, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of KoreaDepartment of Thoracic and Cardiovascular Surgery, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of KoreaDepartment of Molecular Medicine and Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, Seoul 07804, Republic of KoreaDepartment of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Republic of KoreaDivision of Medical Oncology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of KoreaMicroRNA transcriptomes from fresh tumors and the adjacent normal tissues were profiled in 10 Korean patients diagnosed with lung adenocarcinoma using a next-generation sequencing (NGS) technique called miRNA-seq. The sequencing quality was assessed using FastQC, and low-quality or adapter-contaminated portions of the reads were removed using Trim Galore. Quality-assured reads were analyzed using miRDeep2 and Bowtie. The abundance of known miRNAs was estimated using the reads per million (RPM) normalization method. Subsequently, using DESeq2 and Wx, we identified differentially expressed miRNAs and potential miRNA biomarkers for lung adenocarcinoma tissues compared to adjacent normal tissues, respectively. We defined reliable miRNA biomarkers for lung adenocarcinoma as those detected by both methods. The miRNA-seq data are available in the Gene Expression Omnibus (GEO) database under accession number GSE196633, and all processed data can be accessed via the Mendeley data website.https://www.mdpi.com/2306-5729/8/6/94microRNAlung adenocarcinomaKorean patientsnext-generation sequencingmiRNA-seqWx |
| spellingShingle | Jihye Park Sae Jung Na Jung Sook Yoon Seoree Kim Sang Hoon Chun Jae Jun Kim Young-Du Kim Young-Ho Ahn Keunsoo Kang Yoon Ho Ko MicroRNA Profiling of Fresh Lung Adenocarcinoma and Adjacent Normal Tissues from Ten Korean Patients Using miRNA-Seq Data microRNA lung adenocarcinoma Korean patients next-generation sequencing miRNA-seq Wx |
| title | MicroRNA Profiling of Fresh Lung Adenocarcinoma and Adjacent Normal Tissues from Ten Korean Patients Using miRNA-Seq |
| title_full | MicroRNA Profiling of Fresh Lung Adenocarcinoma and Adjacent Normal Tissues from Ten Korean Patients Using miRNA-Seq |
| title_fullStr | MicroRNA Profiling of Fresh Lung Adenocarcinoma and Adjacent Normal Tissues from Ten Korean Patients Using miRNA-Seq |
| title_full_unstemmed | MicroRNA Profiling of Fresh Lung Adenocarcinoma and Adjacent Normal Tissues from Ten Korean Patients Using miRNA-Seq |
| title_short | MicroRNA Profiling of Fresh Lung Adenocarcinoma and Adjacent Normal Tissues from Ten Korean Patients Using miRNA-Seq |
| title_sort | microrna profiling of fresh lung adenocarcinoma and adjacent normal tissues from ten korean patients using mirna seq |
| topic | microRNA lung adenocarcinoma Korean patients next-generation sequencing miRNA-seq Wx |
| url | https://www.mdpi.com/2306-5729/8/6/94 |
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